Job name:

noname(2X39 chain A)

b9a758af-e488-42ae-adee-169a108e464c
Finished
Models Number of gaps:1 Gap lengths: 21
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap
Model 1 Unknot -41870
Model 2 Unknot -41783
Model 3 Unknot -41729
Model 4 Unknot -41566
Model 5 Unknot -41386
Reload
Warning: All models are renumbered - the first residue in the structure has index 1.
Mix & match
Provided protein had only one gap - thus there are no gap-filling combinations to be made.

Warning: JSmol may at times display gaps where there are none - due to some overlaps in models. This does not indicate presence of gaps in downloaded structure!
DOPE (Discrete Optimized Protein Energy) score per residue. The lower the score, the better.
Since DOPE is calculated against the neighbours of a given amino acid, the scores
can vary between unmoved segments of different models. See here for more information.
PDB
code
Chain Entanglement
type
Seq
identity
Total gap
coverage
Total gap
identity
RMSD [Å] Pairwise alignment to the target: gap


3D0E

A

Unknot

97.22%

33.33%

28.57%

0.66

..Target: KVTMNDFDYLKLLGKGTFGKVILVREKATGRYYAMKILRKEVIIAKDEVAHTVTESRVLQNTRHPFLTALKYAFQTHDRLCFVMEYANGGELFFHLSRERVFTEERARFYGAEIVSALEYLHSRDVVYRDIKLENLMLDKDGHIKITDFGLCKEGISDGATMKXFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHERLFELILMEEIRFPRTLSPEAKSLLAGLLKKDPKQRLGGGPSDAKEVMEHRFFLSINWQDVVQKKLLPPFKPQVTSEVDTRYFDDEFTAQSITITPPDRYDSLGLLELDQREEQEMFEDFDYIAD-W
Template: KVTMNDFDYLKLLGKGTFGKVILVREKATGRYYAMKILRKEVIIAKDEVAHTVTESRVLQNTRHPFLTALKYAFQTHDRLCFVMEYANGGELFFHLSRERVFTEERARFYGAEIVSALEYLHSRDVVYRDIKLENLMLDKDGHIKITDFGLCKEGISDGATMKXFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHERLFELILMEEIRFPRTLSPEAKSLLAGLLKKDPKQRLGGGPSDAKEVMEHRFFLSINWQDVVQKKLLPPFKPQVTSEVDTRYFDDEFTAQSITIXPPD-----------QR---THFPQFDYSASIR

PDB
code
Chain Knot
type
Gap
coverage
Gap
identity
>Target_Sequence: gap

SITITPPDRYDSLGLLELDQREEQEMF

3D0E A Unknot 28.57% 33.33%

SITIXPPD-----------QR---THF


Sun Jul 23 14:59:38 2017	JOB CREATED : b9a758af-e488-42ae-adee-169a108e464c
Mon Jul 24 00:58:02 2017	STATUS CHANGED : N -> R
Mon Jul 24 00:58:02 2017	INFO : JOB STARTED AT: 2017-07-24 00:58:02.289491
Mon Jul 24 00:58:02 2017	INFO : METHOD: 1
Mon Jul 24 00:58:02 2017	INFO : Precalculated profile found...
Mon Jul 24 00:58:02 2017	INFO : Homologue pool found...
Mon Jul 24 00:58:02 2017	INFO : Verifying structure sequences of homologues...
Mon Jul 24 03:33:56 2017	INFO : Starting homologue filtering...
Mon Jul 24 03:35:03 2017	INFO : Getting structures from PDB...
Mon Jul 24 03:35:09 2017	INFO : Creating modelling alignment...
Mon Jul 24 03:35:09 2017	INFO : Modelling...
Mon Jul 24 03:38:46 2017	INFO : Model 1 built
Mon Jul 24 03:38:46 2017	INFO : Validating Calpha distances...
Mon Jul 24 03:38:46 2017	INFO : Model 1 distances correct: True
Mon Jul 24 03:38:46 2017	INFO : Modelling...
Mon Jul 24 03:42:20 2017	INFO : Model 2 built
Mon Jul 24 03:42:20 2017	INFO : Validating Calpha distances...
Mon Jul 24 03:42:20 2017	INFO : Model 2 distances correct: True
Mon Jul 24 03:42:20 2017	INFO : Modelling...
Mon Jul 24 03:46:02 2017	INFO : Model 3 built
Mon Jul 24 03:46:02 2017	INFO : Validating Calpha distances...
Mon Jul 24 03:46:02 2017	INFO : Model 3 distances correct: True
Mon Jul 24 03:46:02 2017	INFO : Modelling...
Mon Jul 24 03:49:42 2017	INFO : Model 4 built
Mon Jul 24 03:49:42 2017	INFO : Validating Calpha distances...
Mon Jul 24 03:49:42 2017	INFO : Model 4 distances correct: True
Mon Jul 24 03:49:42 2017	INFO : Modelling...
Mon Jul 24 03:53:22 2017	INFO : Model 5 built
Mon Jul 24 03:53:22 2017	INFO : Validating Calpha distances...
Mon Jul 24 03:53:22 2017	INFO : Model 5 distances correct: True
Mon Jul 24 03:53:59 2017	INFO : Finished modelling
Mon Jul 24 03:53:59 2017	STATUS CHANGED : R -> P
Mon Jul 24 03:53:59 2017	INFO : Checking topology...
Mon Jul 24 03:58:46 2017	INFO : Knot matrices done...
Mon Jul 24 03:58:46 2017	INFO : No knots found...
Mon Jul 24 03:58:46 2017	INFO : No lassos found...
Mon Jul 24 03:58:46 2017	INFO : Finishing...
Mon Jul 24 03:58:46 2017	INFO : Job done
Mon Jul 24 03:58:46 2017	STATUS CHANGED : P -> F
Mon Jul 24 03:58:46 2017	STATUS CHANGED : F -> F

GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling